The Experts below are selected from a list of 288 Experts worldwide ranked by ideXlab platform
Jinxian Liu - One of the best experts on this subject based on the ideXlab platform.
-
population genomic signatures of genetic structure and environmental selection in the Catadromous roughskin sculpin trachidermus fasciatus
Genome Biology and Evolution, 2019Co-Authors: Dongxiu Xue, Baidong Zhang, Jinxian LiuAbstract:Understanding the patterns of genetic diversity and adaptation across species' range is crucial to assess its long-term persistence and determine appropriate conservation measures. The impacts of human activities on the genetic diversity and genetic adaptation to heterogeneous environments remain poorly understood in the marine realm. The roughskin sculpin (Trachidermus fasciatus) is a small Catadromous Fish, and has been listed as a second-class state protected aquatic animal since 1988 in China. To elucidate the underlying mechanism of population genetic structuring and genetic adaptations to local environments, RAD tags were sequenced for 202 individuals in nine populations across the range of T. fasciatus in China. The pairwise FST values over 9,271 filtered SNPs were significant except that between Dongying and Weifang. All the genetic clustering analysis revealed significant population structure with high support for eight distinct genetic clusters. Both the minor allele frequency spectra and Ne estimations suggested extremely small Ne in some populations (e.g., Qinhuangdao, Rongcheng, Wendeng, and Qingdao), which might result from recent population bottleneck. The strong genetic structure can be partly attributed to genetic drift and habitat fragmentation, likely due to the anthropogenic activities. Annotations of candidate adaptive loci suggested that genes involved in metabolism, development, and osmoregulation were critical for adaptation to spatially heterogenous environment of local populations. In the context of anthropogenic activities and environmental change, results of the present population genomic work provided important contributions to the understanding of genetic differentiation and adaptation to changing environments.
-
genetic diversity and population structure of the roughskin sculpin trachidermus fasciatus heckel inferred from microsatellite analyses implications for its conservation and management
Conservation Genetics, 2016Co-Authors: Dongxiu Xue, Tianxiang Gao, Jinxian LiuAbstract:Identification of population units is crucial for management and monitoring programs, especially for endangered wild species. The roughskin sculpin (Trachidermus fasciatus Heckel) is a small Catadromous Fish and has been listed as a second class state protected aquatic animal since 1988 in China. To achieve sustainable conservation of this species, it is necessary to clarify the existing genetic structure both between and within populations. Here, population genetic structure among eight populations of T. fasciatus were analyzed by using 16 highly polymorphic microsatellites. High levels of genetic variation were observed in all populations. All pairwise F ST estimates were significant after false discovery rate correction (overall average F ST = 0.054). Furthermore, both STRUCTURE and discriminant analysis of principal components (DAPC) analysis showed that the eight populations were grouped into six clusters. BAYESASS analysis showed generally low recent and asymmetric migration among populations. All these results suggested significant genetic structure across populations. However, there was no isolation by distance relationship among populations, likely resulting from barriers to gene flow created by habitat fragmentation. Our results highlight the need for in situ conservation efforts for T. fasciatus across its entire distribution range, through maximizing habitat size and quality to preserve overall genetic diversity and evolutionary potential.
Shaowu Yin - One of the best experts on this subject based on the ideXlab platform.
-
Environmental salinity influences the branchial expression of TCR pathway related genes based on transcriptome of a Catadromous Fish.
Comparative biochemistry and physiology. Part D Genomics & proteomics, 2021Co-Authors: Quanquan Cao, Hongyu Wang, Chengxu Fan, Yiru Sun, Cheng Jinghao, Peng Chu, Shaowu YinAbstract:Environmental salinity not only affects the physiological processes such as osmoregulation and hormonal control, but also changes the immune system in Fishes. Studies are limited in Fish on the roles of the T cell receptor (TCR)-related genes in relation to changes in environmental salinity. A large group of salinity-challenged transcripts was obtained in gills of marbled eel (Anguilla marmorata). Moreover, bioinformatic ways were used to identify the enriched TCR pathway related genes which were significantly different expressed in fresh water (FW), brackish water (BW) and seawater (SW). Meanwhile, the RT-qPCR results were validated and consistent with the RNA-seq results. TCR a, TCR b, CD45, CD28, PI3K, LCK and LAT were up-regulated when the salinity increases in BW and SW, which connected with the related signaling pathways (Ras-MAPK and PKC pathway). CD4 and Zap70 were down-regulated when the salinity increases in BW and SW, which connected with the PLC pathway. The research offers a novel viewpoint to explore the immune pathways including the TCR pathway in Fish based on transcriptome.
-
The influence of environmental calcium on the branchial morphology in a Catadromous Fish.
Environmental science and pollution research international, 2021Co-Authors: Quanquan Cao, Shaowu YinAbstract:Eels are exposed to Ca2+ changes during migration between seawater and freshwater. The gill is the main organ of active calcium transport and has a large surface area to be particularly sensitive to environmental changes in the aquatic environment. In this research, we focused on the morphological changes of gill tissues when eels are faced with the environmental calcium challenges. Based on the results of hematoxylin and eosin (HE) staining and immunohistochemistry, compared with the control group (normal Ca2+ environment), the filament and lamella lengths and lamellar frequency (LF) appeared higher in high calcium environment and lower in deficient calcium environment, while the lamella width and filamental lamellar surface area (SAFL) decreased in high calcium environment and increased in deficient calcium environment. And there was no difference in the number filaments in first right gill arch in the three Ca2+ water environment. Transmission electron microscopy was employed to examine the ultrastructural changes in gills in different Ca2+ water environment. The nucleus and endoplasmic reticulum had a tendency to expand in calcium-deficient water, but had a tendency to shrink in high-calcium water comparing with the control group. This study provides the support that branchial surface areas are regulated in different Ca2+ waters through a list of calcium transporters including CACNB2.
-
iTRAQ proteomic analysis of salinity acclimation proteins in the gill of tropical marbled eel (Anguilla marmorata)
Fish physiology and biochemistry, 2015Co-Authors: Yihe Jia, Shaowu Yin, Fenfei Liang, Xiaolu Wang, Xiaojun Wang, Li WangAbstract:Osmoregulation plays an important role in the migration process of Catadromous Fish. The osmoregulatory mechanisms of tropical marbled eel (Anguilla marmorata), a typical Catadromous Fish, did not gain sufficient attention, especially at the molecular level. In order to enrich the protein database of A. marmorata, a proteomic analysis has been carried out by iTRAQ technique. Among 1937 identified proteins in gill of marbled eel, the expression of 1560 proteins (80 %) was quantified. Compared with the protein expression level in the gill of marbled eel in freshwater (salinity of 0 ‰), 336 proteins were up-regulated and 67 proteins were down-regulated in seawater (salinity of 25 ‰); 33 proteins were up-regulated and 32 proteins were down-regulated in brackish water (salinity of 10 ‰). These up-regulated proteins including Na+/K+-ATPase, V-type proton ATPase, sodium–potassium–chloride co-transporter and heat shock protein 90 were enriched in many KEGG-annotated pathways, which are related to different functions of the gill. The up-regulated oxidative phosphorylation and seleno-compound metabolism pathways involve the synthesis and consumption of ATP, which represents extra energy consumption. Another identified pathway is the ribosome pathway in which a large number of up-regulated proteins are involved. It is also more notable that tight junction and cardiac muscle contraction pathways may have correlation with ion transport in gill cells. This is the first report describing the proteome of A. marmorata for acclimating to the change of salinity. These results provide a functional database for migratory Fish and point out some possible new interactions on osmoregulation in A. marmorata.
Tianxiang Gao - One of the best experts on this subject based on the ideXlab platform.
-
genetic diversity and population structure of the roughskin sculpin trachidermus fasciatus heckel inferred from microsatellite analyses implications for its conservation and management
Conservation Genetics, 2016Co-Authors: Dongxiu Xue, Tianxiang Gao, Jinxian LiuAbstract:Identification of population units is crucial for management and monitoring programs, especially for endangered wild species. The roughskin sculpin (Trachidermus fasciatus Heckel) is a small Catadromous Fish and has been listed as a second class state protected aquatic animal since 1988 in China. To achieve sustainable conservation of this species, it is necessary to clarify the existing genetic structure both between and within populations. Here, population genetic structure among eight populations of T. fasciatus were analyzed by using 16 highly polymorphic microsatellites. High levels of genetic variation were observed in all populations. All pairwise F ST estimates were significant after false discovery rate correction (overall average F ST = 0.054). Furthermore, both STRUCTURE and discriminant analysis of principal components (DAPC) analysis showed that the eight populations were grouped into six clusters. BAYESASS analysis showed generally low recent and asymmetric migration among populations. All these results suggested significant genetic structure across populations. However, there was no isolation by distance relationship among populations, likely resulting from barriers to gene flow created by habitat fragmentation. Our results highlight the need for in situ conservation efforts for T. fasciatus across its entire distribution range, through maximizing habitat size and quality to preserve overall genetic diversity and evolutionary potential.
-
The loss of genetic diversity during captive breeding of the endangered sculpin, Trachidermus fasciatus , based on ISSR markers: implications for its conservation
Chinese Journal of Oceanology and Limnology, 2011Co-Authors: Qiaoli Yang, Tianxiang GaoAbstract:Inter-simple sequence repeat (ISSR) markers were used to determine the genetic variation and genetic differentiation of cultured and wild populations of Trachidermus fasciatus, an endangered Catadromous Fish species in China. Six selected primers were used to amplify DNA samples from 85 individuals, and 353 loci were detected. Relatively low genetic diversity was detected in the cultured population (the percentage of polymorphic loci PPL = 73.80%, Nei’s gene diversity h = 0.178 2, Shannon information index I = 0.276 9). However, the genetic diversity at the species level was relatively high (PPL = 91.78%; h = 0.258 3, I = 0.398 6). The UPGMA tree grouped together the genotypes almost according to their cultured and wild origin, showing distinct differences in genetic structure between wild and cultured populations. The pairwise Fst values confirmed significant genetic differentiation between wild and cultured samples. The cultivated population seems to be low in genetic diversity as a result of detrimental genetic effects in the captive population. The results suggest that ISSR markers are effective for rapid assessment of the degree of diversity of a population, thus giving important topical information relevant to preserving endangered species.
-
Development and characterization of fourteen microsatellite loci in a threatened Catadromous Fish Trachidermus fasciatus
Conservation Genetics Resources, 2011Co-Authors: Guijing Ren, Zhenmin Bao, Tianxiang GaoAbstract:Trachidermus fasciatus (roughskin sculpin), is a Catadromous Fish distributed along southern coasts of Korean Peninsula, coast of China and Japan. Fourteen microsatellite loci were isolated and characterized for this species. Number of alleles ranged from 8 to 18 per locus, and the observed and expected heterozygosity ranged between 0.682–1.000 and 0.853–0.953, respectively. No evidence of linkage disequilibrium was detected. The significant departures from Hardy–Weinberg expectations at two loci suggested the presence of null alleles. These microsatellite loci will be useful for studying population genetic variation.
Dongxiu Xue - One of the best experts on this subject based on the ideXlab platform.
-
population genomic signatures of genetic structure and environmental selection in the Catadromous roughskin sculpin trachidermus fasciatus
Genome Biology and Evolution, 2019Co-Authors: Dongxiu Xue, Baidong Zhang, Jinxian LiuAbstract:Understanding the patterns of genetic diversity and adaptation across species' range is crucial to assess its long-term persistence and determine appropriate conservation measures. The impacts of human activities on the genetic diversity and genetic adaptation to heterogeneous environments remain poorly understood in the marine realm. The roughskin sculpin (Trachidermus fasciatus) is a small Catadromous Fish, and has been listed as a second-class state protected aquatic animal since 1988 in China. To elucidate the underlying mechanism of population genetic structuring and genetic adaptations to local environments, RAD tags were sequenced for 202 individuals in nine populations across the range of T. fasciatus in China. The pairwise FST values over 9,271 filtered SNPs were significant except that between Dongying and Weifang. All the genetic clustering analysis revealed significant population structure with high support for eight distinct genetic clusters. Both the minor allele frequency spectra and Ne estimations suggested extremely small Ne in some populations (e.g., Qinhuangdao, Rongcheng, Wendeng, and Qingdao), which might result from recent population bottleneck. The strong genetic structure can be partly attributed to genetic drift and habitat fragmentation, likely due to the anthropogenic activities. Annotations of candidate adaptive loci suggested that genes involved in metabolism, development, and osmoregulation were critical for adaptation to spatially heterogenous environment of local populations. In the context of anthropogenic activities and environmental change, results of the present population genomic work provided important contributions to the understanding of genetic differentiation and adaptation to changing environments.
-
genetic diversity and population structure of the roughskin sculpin trachidermus fasciatus heckel inferred from microsatellite analyses implications for its conservation and management
Conservation Genetics, 2016Co-Authors: Dongxiu Xue, Tianxiang Gao, Jinxian LiuAbstract:Identification of population units is crucial for management and monitoring programs, especially for endangered wild species. The roughskin sculpin (Trachidermus fasciatus Heckel) is a small Catadromous Fish and has been listed as a second class state protected aquatic animal since 1988 in China. To achieve sustainable conservation of this species, it is necessary to clarify the existing genetic structure both between and within populations. Here, population genetic structure among eight populations of T. fasciatus were analyzed by using 16 highly polymorphic microsatellites. High levels of genetic variation were observed in all populations. All pairwise F ST estimates were significant after false discovery rate correction (overall average F ST = 0.054). Furthermore, both STRUCTURE and discriminant analysis of principal components (DAPC) analysis showed that the eight populations were grouped into six clusters. BAYESASS analysis showed generally low recent and asymmetric migration among populations. All these results suggested significant genetic structure across populations. However, there was no isolation by distance relationship among populations, likely resulting from barriers to gene flow created by habitat fragmentation. Our results highlight the need for in situ conservation efforts for T. fasciatus across its entire distribution range, through maximizing habitat size and quality to preserve overall genetic diversity and evolutionary potential.
Jan Breine - One of the best experts on this subject based on the ideXlab platform.
-
modelling the migration opportunities of diadromous Fish species along a gradient of dissolved oxygen concentration in a european tidal watershed
Estuarine Coastal and Shelf Science, 2007Co-Authors: Joachim Maes, Maarten Stevens, Jan BreineAbstract:The relationship between poor water quality and migration opportunities for Fish remains poorly documented, although it is an essential research step in implementing EU water legislation. In this paper, we model the environmental constraints that control the movements of anadromous and Catadromous Fish populations that migrate through the tidal watershed of River Scheldt, a heavily impacted river basin in Western Europe. Local populations of sturgeon, sea lamprey, sea trout, Atlantic salmon, houting and allis shad were essentially extirpated around 1900. For remaining populations (flounder, three-spined stickleback, twaite shad, thinlip mullet, European eel and European smelt), a data driven logistic model was parameterized. The presence or absence of Fish species in samples taken between 1995 and 2004 was modelled as a function of temperature, dissolved oxygen concentration, river flow and season. Probabilities to catch individuals from all diadromous species but three-spined stickleback increased as a function of the interaction between temperature and dissolved oxygen. The hypoxic zone situated in the freshwater tidal part of the estuary was an effective barrier for upstream migrating anadromous spawners since it blocked the entrance to historical spawning sites upstream. Similarly, habitat availability for Catadromous Fish was greatly reduced and restricted to lower brackish water parts of the estuary. The model was applied to infer preliminary dissolved oxygen criteria for diadromous Fish, to make qualitative predictions about future changes in Fish distribution given anticipated changes in water quality and to suggest necessary measures with respect to watershed management.